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To KKW, Chow JCH, Cheung KM, Cho WCS. Circumvention of Gefitinib Resistance by Repurposing Flunarizine via Histone Deacetylase Inhibition. ACS Pharmacol Transl Sci 2023; 6:1531-1543. [PMID: 37854628 PMCID: PMC10580381 DOI: 10.1021/acsptsci.3c00202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Indexed: 10/20/2023]
Abstract
Gefitinib is an epidermal growth factor receptor tyrosine kinase inhibitor (EGFR TKI) for treating advanced non-small cell lung cancer (NSCLC). However, drug resistance seriously impedes the clinical efficacy of gefitinib. This study investigated the repositioning of the non-oncology drug capable of inhibiting histone deacetylases (HDACs) to overcome gefitinib resistance. A few drug candidates were identified using the in silico repurposing tool "DRUGSURV" and tested for HDAC inhibition. Flunarizine, originally indicated for migraine prophylaxis and vertigo treatment, was selected for detailed investigation in NSCLC cell lines harboring a range of different gefitinib resistance mechanisms (EGFR T790M, KRAS G12S, MET amplification, or PTEN loss). The circumvention of gefitinib resistance by flunarizine was further demonstrated in an EGFR TKI (erlotinib)-refractory patient-derived tumor xenograft (PDX) model in vivo. The acetylation level of cellular histone protein was increased by flunarizine in a concentration- and time-dependent manner. Among the NSCLC cell lines evaluated, the extent of gefitinib resistance circumvention by flunarizine was found to be the most pronounced in EGFR T790M-bearing H1975 cells. The gefitinib-flunarizine combination was shown to induce the apoptotic protein Bim but reduce the antiapoptotic protein Bcl-2, which apparently circumvented gefitinib resistance. The induction of Bim by flunarizine was accompanied by an increase in the histone acetylation and E2F1 interaction with the BIM gene promoter. Flunarizine was also found to upregulate E-cadherin but downregulate the vimentin expression, which subsequently inhibited cancer cell migration and invasion. Importantly, flunarizine was also shown to significantly potentiate the tumor growth suppressive effect of gefitinib in EGFR TKI-refractory PDX in vivo. The findings advocate for the translational application of flunarizine to circumvent gefitinib resistance in the clinic.
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Affiliation(s)
- Kenneth K. W. To
- School
of Pharmacy, Faculty of Medicine, The Chinese
University of Hong Kong, Hong Kong, SAR, China
| | - James C. H. Chow
- Department
of Clinical Oncology, Queen Elizabeth Hospital, Hong Kong, SAR, China
| | - Ka-Man Cheung
- Department
of Clinical Oncology, Queen Elizabeth Hospital, Hong Kong, SAR, China
| | - William C. S. Cho
- Department
of Clinical Oncology, Queen Elizabeth Hospital, Hong Kong, SAR, China
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2
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To KKW, Cheung KM, Cho WCS. Repurposing of triamterene as a histone deacetylase inhibitor to overcome cisplatin resistance in lung cancer treatment. J Cancer Res Clin Oncol 2023; 149:7217-7234. [PMID: 36905422 DOI: 10.1007/s00432-023-04641-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 02/07/2023] [Indexed: 03/12/2023]
Abstract
PURPOSE Cisplatin is the core chemotherapeutic drug used for first-line treatment of advanced non-small cell lung cancer (NSCLC). However, drug resistance is severely hindering its clinical efficacy. This study investigated the circumvention of cisplatin resistance by repurposing non-oncology drugs with putative histone deacetylase (HDAC) inhibitory effect. METHODS A few clinically approved drugs were identified by a computational drug repurposing tool called "DRUGSURV" and evaluated for HDAC inhibition. Triamterene, originally indicated as a diuretic, was chosen for further investigation in pairs of parental and cisplatin-resistant NSCLC cell lines. Sulforhodamine B assay was used to evaluate cell proliferation. Western blot analysis was performed to examine histone acetylation. Flow cytometry was used to examine apoptosis and cell cycle effects. Chromatin immunoprecipitation was conducted to investigate the interaction of transcription factors to the promoter of genes regulating cisplatin uptake and cell cycle progression. The circumvention of cisplatin resistance by triamterene was further verified in a patient-derived tumor xenograft (PDX) from a cisplatin-refractory NSCLC patient. RESULTS Triamterene was found to inhibit HDACs. It was shown to enhance cellular cisplatin accumulation and potentiate cisplatin-induced cell cycle arrest, DNA damage, and apoptosis. Mechanistically, triamterene was found to induce histone acetylation in chromatin, thereby reducing the association of HDAC1 but promoting the interaction of Sp1 with the gene promoter of hCTR1 and p21. Triamterene was further shown to potentiate the anti-cancer effect of cisplatin in cisplatin-resistant PDX in vivo. CONCLUSION The findings advocate further clinical evaluation of the repurposing use of triamterene to overcome cisplatin resistance.
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Affiliation(s)
- Kenneth K W To
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Room 801N, Lo Kwee-Seong Integrated Biomedical Sciences Building, Area 39, Shatin, New Territories, Hong Kong SAR, China.
| | - Ka M Cheung
- Department of Clinical Oncology, Queen Elizabeth Hospital, Hong Kong SAR, China
| | - William C S Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, Hong Kong SAR, China
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3
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Azuma I, Mizuno T, Kusuhara H. NRBdMF: A Recommendation Algorithm for Predicting Drug Effects Considering Directionality. J Chem Inf Model 2023; 63:474-483. [PMID: 36635231 DOI: 10.1021/acs.jcim.2c01210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Predicting the novel effects of drugs based on information about approved drugs can be regarded as a recommendation system. Matrix factorization is one of the most used recommendation systems, and various algorithms have been devised for it. A literature survey and summary of existing algorithms for predicting drug effects demonstrated that most such methods, including neighborhood regularized logistic matrix factorization, which was the best performer in benchmark tests, used a binary matrix that considers only the presence or absence of interactions. However, drug effects are known to have two opposite aspects, such as side effects and therapeutic effects. In the present study, we proposed using neighborhood regularized bidirectional matrix factorization (NRBdMF) to predict drug effects by incorporating bidirectionality, which is a characteristic property of drug effects. We used this proposed method for predicting side effects using a matrix that considered the bidirectionality of drug effects, in which known side effects were assigned a positive (+1) label and known treatment effects were assigned a negative (-1) label. The NRBdMF model, which utilizes drug bidirectional information, achieved enrichment of side effects at the top and indications at the bottom of the prediction list. This first attempt to consider the bidirectional nature of drug effects using NRBdMF showed that it reduced false positives and produced a highly interpretable output.
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Affiliation(s)
- Iori Azuma
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo113-0033, Japan
| | - Tadahaya Mizuno
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo113-0033, Japan
| | - Hiroyuki Kusuhara
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo113-0033, Japan
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4
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Chen YH, Shih YT, Chien CS, Tsai CS. Predicting adverse drug effects: A heterogeneous graph convolution network with a multi-layer perceptron approach. PLoS One 2022; 17:e0266435. [PMID: 36516131 PMCID: PMC9750037 DOI: 10.1371/journal.pone.0266435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 11/19/2022] [Indexed: 12/15/2022] Open
Abstract
We apply a heterogeneous graph convolution network (GCN) combined with a multi-layer perceptron (MLP) denoted by GCNMLP to explore the potential side effects of drugs. Here the SIDER, OFFSIDERS, and FAERS are used as the datasets. We integrate the drug information with similar characteristics from the datasets of known drugs and side effect networks. The heterogeneous graph networks explore the potential side effects of drugs by inferring the relationship between similar drugs and related side effects. This novel in silico method will shorten the time spent in uncovering the unseen side effects within routine drug prescriptions while highlighting the relevance of exploring drug mechanisms from well-documented drugs. In our experiments, we inquire about the drugs Vancomycin, Amlodipine, Cisplatin, and Glimepiride from a trained model, where the parameters are acquired from the dataset SIDER after training. Our results show that the performance of the GCNMLP on these three datasets is superior to the non-negative matrix factorization method (NMF) and some well-known machine learning methods with respect to various evaluation scales. Moreover, new side effects of drugs can be obtained using the GCNMLP.
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Affiliation(s)
- Y.-H. Chen
- Dept. of Nephrology, Taichung Tzu Chi Hospital, Taichung, Taiwan
- School of Medicine, Tzu Chi University, Hualien, Taiwan
| | - Y.-T. Shih
- Dept. of Applied Mathematics, National Chung Hsing University, Taichung, Taiwan
- * E-mail:
| | - C.-S. Chien
- Dept. of Applied Mathematics, National Chung Hsing University, Taichung, Taiwan
| | - C.-S. Tsai
- Dept. of Management of Information Systems, National Chung Hsing University, Taichung, Taiwan
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5
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Identification of Drug-Disease Associations Using a Random Walk with Restart Method and Supervised Learning. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022; 2022:7035634. [PMID: 36262874 PMCID: PMC9576438 DOI: 10.1155/2022/7035634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 09/23/2022] [Indexed: 11/17/2022]
Abstract
Drug-disease correlations play an important role in revealing the mechanism of disease, finding new indications of available drugs, or drug repositioning. A variety of computational approaches were proposed to find drug-disease correlations and achieve good performances. However, these methods used a variety of network information, but integrated networks were rarely used. In addition, the role of known drug-disease association data has not been fully played. In this work, we designed a combination algorithm of random walk and supervised learning to find the drug-disease correlations. We used an integrated network to update the model and selected a gene set as the start of random walk based on the known drug-disease correlations data. The experimental results show that the proposed method can effectively find the correlation between drugs and diseases, and the prediction accuracy is 82.7%. We found that there are 8 pairs of drug-disease relationships that have not yet been reported, and 5 of them have pharmacodynamic effects on Parkinson's disease. We also found that a key linkage between Parkinson's disease and phenylhexol, a drug for the treatment of Parkinson's disease α-synuclein and tau protein, provides a useful exploration for the effectiveness of the treatment of Parkinson's disease.
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Jung YL, Yoo HS, Hwang J. Artificial intelligence-based decision support model for new drug development planning. EXPERT SYSTEMS WITH APPLICATIONS 2022; 198:116825. [PMID: 35283560 PMCID: PMC8902892 DOI: 10.1016/j.eswa.2022.116825] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 01/18/2022] [Accepted: 03/02/2022] [Indexed: 06/14/2023]
Abstract
New drug development guarantees a very high return on success, but the success rate is extremely low. Pharmaceutical companies have attempted to use various strategies to increase the success rate of drug development, but this goal has been difficult to achieve. In this study, we developed a model that can guide effective decision-making at the planning stage of new drug development by leveraging machine learning. The Drug Development Recommendation (DDR) model, we present here, is a hybrid model for recommending and/or predicting drug groups suitable for development by individual pharmaceutical companies. It combines association rule learning, collaborative filtering, and content-based filtering approaches for enterprise-customized recommendations. In the case of content-based filtering applying a random forest classification algorithm, the accuracy and area under curve were 78% and 0.74, respectively. In particular, the DDR model was applied to predict the success probability of companies developing Coronavirus disease 2019 (COVID-19) vaccines. It was demonstrated that the higher the predicted score from the DDR model, the more progress in the clinical phase of the COVID-19 vaccine development. Although our approach has limitations that should be improved, it makes scientific as well as industrial contributions in that the DDR model can support rational decision-making prior to initiating drug development by considering not only technical aspects but also company-related variables.
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Affiliation(s)
- Ye Lim Jung
- Division of Data Analysis, Korea Institute of Science and Technology Information (KISTI), Seoul 02456, Republic of Korea
| | - Hyoung Sun Yoo
- Division of Data Analysis, Korea Institute of Science and Technology Information (KISTI), Seoul 02456, Republic of Korea
- Science and Technology Management Policy, University of Science and Technology, Daejeon 34113, Republic of Korea
| | - JeeNa Hwang
- Division of Data Analysis, Korea Institute of Science and Technology Information (KISTI), Seoul 02456, Republic of Korea
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7
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Allahgholi M, Rahmani H, Javdani D, Sadeghi-Adl Z, Bender A, Módos D, Weiss G. DDREL: From drug-drug relationships to drug repurposing. INTELL DATA ANAL 2022. [DOI: 10.3233/ida-215745] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Analyzing the relationships among various drugs is an essential issue in the field of computational biology. Different kinds of informative knowledge, such as drug repurposing, can be extracted from drug-drug relationships. Scientific literature represents a rich source for the retrieval of knowledge about the relationships between biological concepts, mainly drug-drug, disease-disease, and drug-disease relationships. In this paper, we propose DDREL as a general-purpose method that applies deep learning on scientific literature to automatically extract the graph of syntactic and semantic relationships among drugs. DDREL remarkably outperforms the existing human drug network method and a random network respected to average similarities of drugs’ anatomical therapeutic chemical (ATC) codes. DDREL is able to shed light on the existing deficiency of the ATC codes in various drug groups. From the DDREL graph, the history of drug discovery became visible. In addition, drugs that had repurposing score 1 (diflunisal, pargyline, fenofibrate, guanfacine, chlorzoxazone, doxazosin, oxymetholone, azathioprine, drotaverine, demecarium, omifensine, yohimbine) were already used in additional indication. The proposed DDREL method justifies the predictive power of textual data in PubMed abstracts. DDREL shows that such data can be used to 1- Predict repurposing drugs with high accuracy, and 2- Reveal existing deficiencies of the ATC codes in various drug groups.
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Affiliation(s)
- Milad Allahgholi
- School of Computer Engineering, Iran University of Science and Technology, Tehran, Iran
| | - Hossein Rahmani
- School of Computer Engineering, Iran University of Science and Technology, Tehran, Iran
| | - Delaram Javdani
- School of Computer Engineering, Iran University of Science and Technology, Tehran, Iran
| | - Zahra Sadeghi-Adl
- School of Computer Engineering, Iran University of Science and Technology, Tehran, Iran
| | - Andreas Bender
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Dezsö Módos
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, UK
- Earlham Institute, Norwich Research Park, Norwich, Norfolk, UK
| | - Gerhard Weiss
- Department of Data Science and Knowledge Engineering (DKE), Maastricht University, Maastricht, The Netherlands
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8
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ADDI: Recommending alternatives for drug-drug interactions with negative health effects. Comput Biol Med 2020; 125:103969. [PMID: 32836102 DOI: 10.1016/j.compbiomed.2020.103969] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 08/09/2020] [Accepted: 08/09/2020] [Indexed: 11/21/2022]
Abstract
Investigating the interactions among various drugs is an indispensable issue in the field of computational biology. Scientific literature represents a rich source for the retrieval of knowledge about the interactions between drugs. Predicting drug-drug interaction (DDI) types will help biologists to evade hazardous drug interactions and support them in discovering potential alternatives that increase therapeutic efficacy and reduce toxicity. In this paper, we propose a general-purpose method called ADDI (standing for Alternative Drug-Drug Interaction) that applies deep learning on PubMed abstracts to predict interaction types among drugs. As an application, ADDI recommends alternatives for drug-drug interactions (DDIs) which have Negative Health Effects Types (NHETs). ADDI clearly outperforms state-of-the-art methods, on average by 13%, with respect to accuracy by using only the textual content of the online PubMed papers. Additionally, manual evaluation of ADDI indicates high precision in recommending alternatives for DDIs with NHETs.
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9
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Sosnina EA, Sosnin S, Nikitina AA, Nazarov I, Osolodkin DI, Fedorov MV. Recommender Systems in Antiviral Drug Discovery. ACS OMEGA 2020; 5:15039-15051. [PMID: 32632398 PMCID: PMC7315437 DOI: 10.1021/acsomega.0c00857] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 06/03/2020] [Indexed: 06/11/2023]
Abstract
Recommender systems (RSs), which underwent rapid development and had an enormous impact on e-commerce, have the potential to become useful tools for drug discovery. In this paper, we applied RS methods for the prediction of the antiviral activity class (active/inactive) for compounds extracted from ChEMBL. Two main RS approaches were applied: collaborative filtering (Surprise implementation) and content-based filtering (sparse-group inductive matrix completion (SGIMC) method). The effectiveness of RS approaches was investigated for prediction of antiviral activity classes ("interactions") for compounds and viruses, for which some of their interactions with other viruses or compounds are known, and for prediction of interaction profiles for new compounds. Both approaches achieved relatively good prediction quality for binary classification of individual interactions and compound profiles, as quantified by cross-validation and external validation receiver operating characteristic (ROC) score >0.9. Thus, even simple recommender systems may serve as an effective tool in antiviral drug discovery.
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Affiliation(s)
- Ekaterina A. Sosnina
- Center
for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30/1, Moscow 143026, Russia
- Institute
of Physiologically Active Compounds, RAS, Severniy pr. 1, Chernogolovka 142432, Russia
| | - Sergey Sosnin
- Center
for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30/1, Moscow 143026, Russia
- Syntelly
LLC, Skolkovo Innovation Center, Bolshoy Boulevard 30, Moscow 121205, Russia
| | - Anastasia A. Nikitina
- Department
of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1 bd. 3, Moscow 119991, Russia
- FSBSI
“Chumakov FSC R&D IBP RAS”, Poselok Instituta Poliomielita 8
bd. 1, Poselenie Moskovsky, Moscow 108819, Russia
| | - Ivan Nazarov
- Center
for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30/1, Moscow 143026, Russia
| | - Dmitry I. Osolodkin
- FSBSI
“Chumakov FSC R&D IBP RAS”, Poselok Instituta Poliomielita 8
bd. 1, Poselenie Moskovsky, Moscow 108819, Russia
- Institute
of Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University, Trubetskaya Ulitsa 8, Moscow 119991, Russia
| | - Maxim V. Fedorov
- Center
for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30/1, Moscow 143026, Russia
- Syntelly
LLC, Skolkovo Innovation Center, Bolshoy Boulevard 30, Moscow 121205, Russia
- Physics
John Anderson Building, University of Strathclyde, 107 Rottenrow East, Glasgow G4 0NG, U.K.
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10
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Luo ZH, Shi MW, Yang Z, Zhang HY, Chen ZX. pyMeSHSim: an integrative python package for biomedical named entity recognition, normalization, and comparison of MeSH terms. BMC Bioinformatics 2020; 21:252. [PMID: 32552728 PMCID: PMC7301509 DOI: 10.1186/s12859-020-03583-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 06/04/2020] [Indexed: 01/24/2023] Open
Abstract
Background Many disease causing genes have been identified through different methods, but there have been no uniform annotations of biomedical named entity (bio-NE) of the disease phenotypes of these genes yet. Furthermore, semantic similarity comparison between two bio-NE annotations has become important for data integration or system genetics analysis. Results The package pyMeSHSim recognizes bio-NEs by using MetaMap which produces Unified Medical Language System (UMLS) concepts in natural language process. To map the UMLS concepts to Medical Subject Headings (MeSH), pyMeSHSim is embedded with a house-made dataset containing the main headings (MHs), supplementary concept records (SCRs), and their relations in MeSH. Based on the dataset, pyMeSHSim implemented four information content (IC)-based algorithms and one graph-based algorithm to measure the semantic similarity between two MeSH terms. To evaluate its performance, we used pyMeSHSim to parse OMIM and GWAS phenotypes. The pyMeSHSim introduced SCRs and the curation strategy of non-MeSH-synonymous UMLS concepts, which improved the performance of pyMeSHSim in the recognition of OMIM phenotypes. In the curation of 461 GWAS phenotypes, pyMeSHSim showed recall > 0.94, precision > 0.56, and F1 > 0.70, demonstrating better performance than the state-of-the-art tools DNorm and TaggerOne in recognizing MeSH terms from short biomedical phrases. The semantic similarity in MeSH terms recognized by pyMeSHSim and the previous manual work was calculated by pyMeSHSim and another semantic analysis tool meshes, respectively. The result indicated that the correlation of semantic similarity analysed by two tools reached as high as 0.89–0.99. Conclusions The integrative MeSH tool pyMeSHSim embedded with the MeSH MHs and SCRs realized the bio-NE recognition, normalization, and comparison in biomedical text-mining.
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Affiliation(s)
- Zhi-Hui Luo
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, PR China.,College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, Hubei, 430070, PR China
| | - Meng-Wei Shi
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, PR China.,College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, Hubei, 430070, PR China
| | - Zhuang Yang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, PR China.,College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, Hubei, 430070, PR China
| | - Hong-Yu Zhang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei, 430070, PR China.
| | - Zhen-Xia Chen
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, PR China. .,College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, Hubei, 430070, PR China.
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11
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Lau A, So HC. Turning genome-wide association study findings into opportunities for drug repositioning. Comput Struct Biotechnol J 2020; 18:1639-1650. [PMID: 32670504 PMCID: PMC7334463 DOI: 10.1016/j.csbj.2020.06.015] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Revised: 06/05/2020] [Accepted: 06/05/2020] [Indexed: 02/02/2023] Open
Abstract
Drug development is a very costly and lengthy process, while repositioned or repurposed drugs could be brought into clinical practice within a shorter time-frame and at a much reduced cost. Numerous computational approaches to drug repositioning have been developed, but methods utilizing genome-wide association studies (GWASs) data are less explored. The past decade has observed a massive growth in the amount of data from GWAS; the rich information contained in GWAS has great potential to guide drug repositioning or discovery. While multiple tools are available for finding the most relevant genes from GWAS hits, searching for top susceptibility genes is only one way to guide repositioning, which has its own limitations. Here we provide a comprehensive review of different computational approaches that employ GWAS data to guide drug repositioning. These methods include selecting top candidate genes from GWAS as drug targets, deducing drug candidates based on drug-drug and disease-disease similarities, searching for reversed expression profiles between drugs and diseases, pathway-based methods as well as approaches based on analysis of biological networks. Each method is illustrated with examples, and their respective strengths and limitations are discussed. We also discussed several areas for future research.
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Affiliation(s)
- Alexandria Lau
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Hon-Cheong So
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
- KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research of Common Diseases, Kunming Zoology Institute of Zoology and The Chinese University of Hong Kong, Hong Kong SAR, China
- Department of Psychiatry, The Chinese University of Hong Kong, Hong Kong SAR, China
- Margaret K.L. Cheung Research Centre for Management of Parkinsonism, The Chinese University of Hong Kong, Hong Kong SAR, China
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
- Brain and Mind Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
- Hong Kong Branch of the Chinese Academy of Sciences Center for Excellence in Animal Evolution and Genetics, The Chinese University of Hong Kong, Hong Kong SAR, China
- Corresponding author at: School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China.
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12
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Jerome RN, Joly MM, Kennedy N, Shirey-Rice JK, Roden DM, Bernard GR, Holroyd KJ, Denny JC, Pulley JM. Leveraging Human Genetics to Identify Safety Signals Prior to Drug Marketing Approval and Clinical Use. Drug Saf 2020; 43:567-582. [PMID: 32112228 PMCID: PMC7398579 DOI: 10.1007/s40264-020-00915-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
INTRODUCTION When a new drug or biologic product enters the market, its full spectrum of side effects is not yet fully understood, as use in the real world often uncovers nuances not suggested within the relatively narrow confines of preapproval preclinical and trial work. OBJECTIVE We describe a new, phenome-wide association study (PheWAS)- and evidence-based approach for detection of potential adverse drug effects. METHODS We leveraged our established platform, which integrates human genetic data with associated phenotypes in electronic health records from 29,722 patients of European ancestry, to identify gene-phenotype associations that may represent known safety issues. We examined PheWAS data and the published literature for 16 genes, each of which encodes a protein targeted by at least one drug or biologic product. RESULTS Initial data demonstrated that our novel approach (safety ascertainment using PheWAS [SA-PheWAS]) can replicate published safety information across multiple drug classes, with validated findings for 13 of 16 gene-drug class pairs. CONCLUSIONS By connecting and integrating in vivo and in silico data, SA-PheWAS offers an opportunity to supplement current methods for predicting or confirming safety signals associated with therapeutic agents.
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Affiliation(s)
- Rebecca N Jerome
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, TN, USA.
| | - Meghan Morrison Joly
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Nan Kennedy
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jana K Shirey-Rice
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Dan M Roden
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Biomedical Informatics, Vanderbilt University, Nashville, TN, USA
| | - Gordon R Bernard
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Kenneth J Holroyd
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, TN, USA
- Center for Technology Transfer and Commercialization, Vanderbilt University, Nashville, TN, USA
| | - Joshua C Denny
- Department of Biomedical Informatics, Vanderbilt University, Nashville, TN, USA
| | - Jill M Pulley
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, TN, USA
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Luo H, Li M, Wang S, Liu Q, Li Y, Wang J. Computational drug repositioning using low-rank matrix approximation and randomized algorithms. Bioinformatics 2019; 34:1904-1912. [PMID: 29365057 DOI: 10.1093/bioinformatics/bty013] [Citation(s) in RCA: 124] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2017] [Accepted: 01/18/2018] [Indexed: 12/26/2022] Open
Abstract
Motivation Computational drug repositioning is an important and efficient approach towards identifying novel treatments for diseases in drug discovery. The emergence of large-scale, heterogeneous biological and biomedical datasets has provided an unprecedented opportunity for developing computational drug repositioning methods. The drug repositioning problem can be modeled as a recommendation system that recommends novel treatments based on known drug-disease associations. The formulation under this recommendation system is matrix completion, assuming that the hidden factors contributing to drug-disease associations are highly correlated and thus the corresponding data matrix is low-rank. Under this assumption, the matrix completion algorithm fills out the unknown entries in the drug-disease matrix by constructing a low-rank matrix approximation, where new drug-disease associations having not been validated can be screened. Results In this work, we propose a drug repositioning recommendation system (DRRS) to predict novel drug indications by integrating related data sources and validated information of drugs and diseases. Firstly, we construct a heterogeneous drug-disease interaction network by integrating drug-drug, disease-disease and drug-disease networks. The heterogeneous network is represented by a large drug-disease adjacency matrix, whose entries include drug pairs, disease pairs, known drug-disease interaction pairs and unknown drug-disease pairs. Then, we adopt a fast Singular Value Thresholding (SVT) algorithm to complete the drug-disease adjacency matrix with predicted scores for unknown drug-disease pairs. The comprehensive experimental results show that DRRS improves the prediction accuracy compared with the other state-of-the-art approaches. In addition, case studies for several selected drugs further demonstrate the practical usefulness of the proposed method. Availability and implementation http://bioinformatics.csu.edu.cn/resources/softs/DrugRepositioning/DRRS/index.html. Contact yaohang@cs.odu.edu or jxwang@mail.csu.edu.cn. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Huimin Luo
- School of Information Science and Engineering, Central South University, ChangSha 410083, China.,School of Computer and Information Engineering, Henan University, KaiFeng 475001, China
| | - Min Li
- School of Information Science and Engineering, Central South University, ChangSha 410083, China
| | - Shaokai Wang
- School of Information Science and Engineering, Central South University, ChangSha 410083, China
| | - Quan Liu
- School of Information Science and Engineering, Central South University, ChangSha 410083, China
| | - Yaohang Li
- Department of Computer Science, Old Dominion University, Norfolk, VA 23529, USA
| | - Jianxin Wang
- School of Information Science and Engineering, Central South University, ChangSha 410083, China
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14
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Systematic analysis of genes and diseases using PheWAS-Associated networks. Comput Biol Med 2019; 109:311-321. [DOI: 10.1016/j.compbiomed.2019.04.037] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 04/28/2019] [Accepted: 04/28/2019] [Indexed: 02/08/2023]
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15
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Long S, Yuan C, Wang Y, Zhang J, Li G. Network Pharmacology Analysis of Damnacanthus indicus C.F.Gaertn in Gene-Phenotype. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE : ECAM 2019; 2019:1368371. [PMID: 30906409 PMCID: PMC6398045 DOI: 10.1155/2019/1368371] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 01/21/2019] [Accepted: 02/03/2019] [Indexed: 12/11/2022]
Abstract
Damnacanthus indicus C.F.Gaertn is known as Huci in traditional Chinese medicine. It contains a component having anthraquinone-like structure which is a part of the many used anticancer drugs. This study was to collect the evidence of disease-modulatory activities of Huci by analyzing the published literature on the chemicals and drugs. A list of its compounds and direct protein targets is predicted by using Bioinformatics Analysis Tool for Molecular Mechanism of TCM. A protein-protein interaction network using links between its directed targets and the other known targets was constructed. The DPT-associated genes in net were scrutinized by WebGestalt. Exploring the cancer genomics data related to Huci through cBio Portal. Survival analysis for the overlap genes is done by using UALCAN. We got 16 compounds and it predicts 62 direct protein targets and 100 DPTs and they were identified for these compounds. DPT-associated genes were analyzed by WebGestalt. Through the enrichment analysis, we got top 10 identified KEGG pathways. Refined analysis of KEGG pathways showed that one of these ten pathways is linked to Rap1 signaling pathway and another one is related to breast cancer. The survival analysis for the overlap genes shows the significant negative effect of these genes on the breast cancer patients. Through the research results of Damnacanthus indicus C.F.Gaertn, it is shown that medicine network pharmacology may be regarded as a new paradigm for guiding the future studies of the traditional Chinese medicine in different fields.
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Affiliation(s)
- Shengrong Long
- Department of Neurosurgery, The First Affiliated Hospital of China Medical University, NanJing Bei Road, Heping District, Shenyang, 110001, LiaoNing Province, China
| | - Caihong Yuan
- Department of Chinese Medicine, The First Affiliated Hospital of China Medical University, NanJing Bei Road, Heping District, Shenyang, 110001, LiaoNing Province, China
| | - Yue Wang
- Department of Neurosurgery, The First Affiliated Hospital of China Medical University, NanJing Bei Road, Heping District, Shenyang, 110001, LiaoNing Province, China
| | - Jie Zhang
- Department of Chinese Medicine, The First Affiliated Hospital of China Medical University, NanJing Bei Road, Heping District, Shenyang, 110001, LiaoNing Province, China
| | - Guangyu Li
- Department of Neurosurgery, The First Affiliated Hospital of China Medical University, NanJing Bei Road, Heping District, Shenyang, 110001, LiaoNing Province, China
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16
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Zhang W, Yue X, Huang F, Liu R, Chen Y, Ruan C. Predicting drug-disease associations and their therapeutic function based on the drug-disease association bipartite network. Methods 2018; 145:51-59. [DOI: 10.1016/j.ymeth.2018.06.001] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 05/15/2018] [Accepted: 06/01/2018] [Indexed: 02/01/2023] Open
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17
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Chuai G, Ma H, Yan J, Chen M, Hong N, Xue D, Zhou C, Zhu C, Chen K, Duan B, Gu F, Qu S, Huang D, Wei J, Liu Q. DeepCRISPR: optimized CRISPR guide RNA design by deep learning. Genome Biol 2018; 19:80. [PMID: 29945655 PMCID: PMC6020378 DOI: 10.1186/s13059-018-1459-4] [Citation(s) in RCA: 226] [Impact Index Per Article: 37.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 05/28/2018] [Indexed: 12/22/2022] Open
Abstract
A major challenge for effective application of CRISPR systems is to accurately predict the single guide RNA (sgRNA) on-target knockout efficacy and off-target profile, which would facilitate the optimized design of sgRNAs with high sensitivity and specificity. Here we present DeepCRISPR, a comprehensive computational platform to unify sgRNA on-target and off-target site prediction into one framework with deep learning, surpassing available state-of-the-art in silico tools. In addition, DeepCRISPR fully automates the identification of sequence and epigenetic features that may affect sgRNA knockout efficacy in a data-driven manner. DeepCRISPR is available at http://www.deepcrispr.net/ .
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Affiliation(s)
- Guohui Chuai
- Department of Endocrinology & Metabolism, Shanghai Tenth People's Hospital, Tongji University, Shanghai, 20009, China
- Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 20009, China
| | - Hanhui Ma
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Jifang Yan
- Department of Endocrinology & Metabolism, Shanghai Tenth People's Hospital, Tongji University, Shanghai, 20009, China
- Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 20009, China
| | - Ming Chen
- R&D Information, Innovation Center China, AstraZeneca, 199 Liangjing Road, Shanghai, 201203, China
| | - Nanfang Hong
- Department of Endocrinology & Metabolism, Shanghai Tenth People's Hospital, Tongji University, Shanghai, 20009, China
- Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 20009, China
| | - Dongyu Xue
- Department of Endocrinology & Metabolism, Shanghai Tenth People's Hospital, Tongji University, Shanghai, 20009, China
- Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 20009, China
| | - Chi Zhou
- Department of Endocrinology & Metabolism, Shanghai Tenth People's Hospital, Tongji University, Shanghai, 20009, China
- Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 20009, China
| | - Chenyu Zhu
- Department of Endocrinology & Metabolism, Shanghai Tenth People's Hospital, Tongji University, Shanghai, 20009, China
- Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 20009, China
| | - Ke Chen
- Department of Endocrinology & Metabolism, Shanghai Tenth People's Hospital, Tongji University, Shanghai, 20009, China
- Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 20009, China
| | - Bin Duan
- Department of Endocrinology & Metabolism, Shanghai Tenth People's Hospital, Tongji University, Shanghai, 20009, China
- Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 20009, China
| | - Feng Gu
- State Key Laboratory Cultivation Base and Key Laboratory of Vision Science, Ministry of Health and Zhejiang Provincial Key Laboratory of Ophthalmology and Optometry, School of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, 325027, China
| | - Sheng Qu
- Department of Endocrinology & Metabolism, Shanghai Tenth People's Hospital, Tongji University, Shanghai, 20009, China
- Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 20009, China
| | - Deshuang Huang
- Machine Learning & Systems Biology Lab, School of Electronics and Information Engineering, Tongji University, Shanghai, 201804, China.
| | - Jia Wei
- R&D Information, Innovation Center China, AstraZeneca, 199 Liangjing Road, Shanghai, 201203, China.
| | - Qi Liu
- Department of Endocrinology & Metabolism, Shanghai Tenth People's Hospital, Tongji University, Shanghai, 20009, China.
- Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 20009, China.
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18
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Zhang W, Yue X, Lin W, Wu W, Liu R, Huang F, Liu F. Predicting drug-disease associations by using similarity constrained matrix factorization. BMC Bioinformatics 2018; 19:233. [PMID: 29914348 PMCID: PMC6006580 DOI: 10.1186/s12859-018-2220-4] [Citation(s) in RCA: 135] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 05/28/2018] [Indexed: 02/06/2023] Open
Abstract
Background Drug-disease associations provide important information for the drug discovery. Wet experiments that identify drug-disease associations are time-consuming and expensive. However, many drug-disease associations are still unobserved or unknown. The development of computational methods for predicting unobserved drug-disease associations is an important and urgent task. Results In this paper, we proposed a similarity constrained matrix factorization method for the drug-disease association prediction (SCMFDD), which makes use of known drug-disease associations, drug features and disease semantic information. SCMFDD projects the drug-disease association relationship into two low-rank spaces, which uncover latent features for drugs and diseases, and then introduces drug feature-based similarities and disease semantic similarity as constraints for drugs and diseases in low-rank spaces. Different from the classic matrix factorization technique, SCMFDD takes the biological context of the problem into account. In computational experiments, the proposed method can produce high-accuracy performances on benchmark datasets, and outperform existing state-of-the-art prediction methods when evaluated by five-fold cross validation and independent testing. Conclusion We developed a user-friendly web server by using known associations collected from the CTD database, available at http://www.bioinfotech.cn/SCMFDD/. The case studies show that the server can find out novel associations, which are not included in the CTD database.
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Affiliation(s)
- Wen Zhang
- School of Computer Science, Wuhan University, Wuhan, 430072, China.
| | - Xiang Yue
- School of Computer Science, Wuhan University, Wuhan, 430072, China
| | - Weiran Lin
- School of Computer Science, Wuhan University, Wuhan, 430072, China
| | - Wenjian Wu
- School of Electronic Information, Wuhan University, Wuhan, 430072, China
| | - Ruoqi Liu
- School of Computer Science, Wuhan University, Wuhan, 430072, China
| | - Feng Huang
- School of Computer Science, Wuhan University, Wuhan, 430072, China
| | - Feng Liu
- School of Computer Science, Wuhan University, Wuhan, 430072, China.
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19
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Musa A, Ghoraie LS, Zhang SD, Glazko G, Yli-Harja O, Dehmer M, Haibe-Kains B, Emmert-Streib F. A review of connectivity map and computational approaches in pharmacogenomics. Brief Bioinform 2018; 19:506-523. [PMID: 28069634 PMCID: PMC5952941 DOI: 10.1093/bib/bbw112] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Large-scale perturbation databases, such as Connectivity Map (CMap) or Library of Integrated Network-based Cellular Signatures (LINCS), provide enormous opportunities for computational pharmacogenomics and drug design. A reason for this is that in contrast to classical pharmacology focusing at one target at a time, the transcriptomics profiles provided by CMap and LINCS open the door for systems biology approaches on the pathway and network level. In this article, we provide a review of recent developments in computational pharmacogenomics with respect to CMap and LINCS and related applications.
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Affiliation(s)
- Aliyu Musa
- Predictive Medicine and Analytics Lab, Department of Signal Processing, Tampere University of Technology, Tampere, Finland
| | - Laleh Soltan Ghoraie
- Bioinformatics and Computational Genomics Laboratory, Princess Margaret Cancer Center, University Health Network, Toronto, ON, Canada
| | - Shu-Dong Zhang
- Northern Ireland Centre for Stratified Medicine, Biomedical Sciences Research Institute, University of Ulster, C-TRIC Building, Altnagelvin Area Hospital, Glenshane Road, Derry/Londonderry, Northern Ireland, UK
| | - Galina Glazko
- University of Rochester Department of Biostatistics and Computational Biology, Rochester, New York, USA
| | - Olli Yli-Harja
- Computational Systems Biology, Department of Signal Processing, Tampere University of Technology, Tampere, Finland
| | - Matthias Dehmer
- Institute for Bioinformatics and Translational Research, UMIT- The Health and Life Sciences University, Eduard Wallnoefer Zentrum 1, Hall in Tyrol, Austria
| | - Benjamin Haibe-Kains
- Bioinformatics and Computational Genomics Laboratory, Princess Margaret Cancer Center, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Department of Computer Science, University of Toronto, Toronto, ON, Canada
- Ontario Institute of Cancer Research, Toronto, ON, Canada
| | - Frank Emmert-Streib
- Predictive Medicine and Analytics Lab, Department of Signal Processing, Tampere University of Technology, Tampere, Finland
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20
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Yu L, Su R, Wang B, Zhang L, Zou Y, Zhang J, Gao L. Prediction of Novel Drugs for Hepatocellular Carcinoma Based on Multi-Source Random Walk. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2017; 14:966-977. [PMID: 27076463 DOI: 10.1109/tcbb.2016.2550453] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Computational approaches for predicting drug-disease associations by integrating gene expression and biological network provide great insights to the complex relationships among drugs, targets, disease genes, and diseases at a system level. Hepatocellular carcinoma (HCC) is one of the most common malignant tumors with a high rate of morbidity and mortality. We provide an integrative framework to predict novel d rugs for HCC based on multi-source random walk (PD-MRW). Firstly, based on gene expression and protein interaction network, we construct a gene-gene weighted i nteraction network (GWIN). Then, based on multi-source random walk in GWIN, we build a drug-drug similarity network. Finally, based on the known drugs for HCC, we score all drugs in the drug-drug similarity network. The robustness of our predictions, their overlap with those reported in Comparative Toxicogenomics Database (CTD) and literatures, and their enriched KEGG pathway demonstrate our approach can effectively identify new drug indications. Specifically, regorafenib (Rank = 9 in top-20 list) is proven to be effective in Phase I and II clinical trials of HCC, and the Phase III trial is ongoing. And, it has 11 overlapping pathways with HCC with lower p-values. Focusing on a particular disease, we believe our approach is more accurate and possesses better scalability.
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21
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Annamanedi M, Varma GYN, Anuradha K, Kalle AM. Celecoxib Enhances the Efficacy of Low-Dose Antibiotic Treatment against Polymicrobial Sepsis in Mice and Clinical Isolates of ESKAPE Pathogens. Front Microbiol 2017; 8:805. [PMID: 28533769 PMCID: PMC5420555 DOI: 10.3389/fmicb.2017.00805] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 04/19/2017] [Indexed: 11/13/2022] Open
Abstract
Treatment of multidrug resistant bacterial infections has been a great challenge globally. Previous studies including our study have highlighted the use of celecoxib, a non-steroidal anti-inflammatory drug in combination with antibiotic has decreased the minimal inhibitory concentration to limit Staphylococcus aureus infection. However, the efficacy of this combinatorial treatment against various pathogenic bacteria is not determined. Therefore, we have evaluated the potential use of celecoxib in combination with low doses of antibiotic in limiting Gram-positive and Gram-negative bacteria in vivo in murine polymicrobial sepsis developed by cecum ligation and puncture (CLP) method and against clinically isolated human ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species). The in vivo results clearly demonstrated a significant reduction in the bacterial load in different organs and in the inflammatory markers such as COX-2 and NF-κB via activation of SIRT1 in mice treated with imipenem, a choice of antibiotic for polymicrobial sepsis treatment. Combinatorial treatment of ampicillin and celecoxib was effective on clinical isolates of ESKAPE pathogens, 45% of tested clinical isolates showed more than 50% reduction in the colony forming units when compared to ampicillin alone. In conclusion, this non-traditional treatment strategy might be effective in clinic to reduce the dose of antibiotic to treat drug-resistant bacterial infections.
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Affiliation(s)
- Madhavi Annamanedi
- Department of Animal Biology, School of Life Sciences, University of HyderabadHyderabad, India
| | - Gajapati Y N Varma
- Department of Animal Biology, School of Life Sciences, University of HyderabadHyderabad, India
| | - K Anuradha
- Pathology and Lab Medicine, Asian Institute of GastroenterologyHyderabad, India
| | - Arunasree M Kalle
- Department of Animal Biology, School of Life Sciences, University of HyderabadHyderabad, India
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22
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Yu L, Wang B, Ma X, Gao L. The extraction of drug-disease correlations based on module distance in incomplete human interactome. BMC SYSTEMS BIOLOGY 2016; 10:111. [PMID: 28155709 PMCID: PMC5260043 DOI: 10.1186/s12918-016-0364-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
BACKGROUND Extracting drug-disease correlations is crucial in unveiling disease mechanisms, as well as discovering new indications of available drugs, or drug repositioning. Both the interactome and the knowledge of disease-associated and drug-associated genes remain incomplete. RESULTS We present a new method to predict the associations between drugs and diseases. Our method is based on a module distance, which is originally proposed to calculate distances between modules in incomplete human interactome. We first map all the disease genes and drug genes to a combined protein interaction network. Then based on the module distance, we calculate the distances between drug gene sets and disease gene sets, and take the distances as the relationships of drug-disease pairs. We also filter possible false positive drug-disease correlations by p-value. Finally, we validate the top-100 drug-disease associations related to six drugs in the predicted results. CONCLUSION The overlapping between our predicted correlations with those reported in Comparative Toxicogenomics Database (CTD) and literatures, and their enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways demonstrate our approach can not only effectively identify new drug indications, but also provide new insight into drug-disease discovery.
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Affiliation(s)
- Liang Yu
- School of Computer Science and Technology, Xidian University, Xi'an, 710071, People's Republic of China.
| | - Bingbo Wang
- School of Computer Science and Technology, Xidian University, Xi'an, 710071, People's Republic of China
| | - Xiaoke Ma
- School of Computer Science and Technology, Xidian University, Xi'an, 710071, People's Republic of China
| | - Lin Gao
- School of Computer Science and Technology, Xidian University, Xi'an, 710071, People's Republic of China
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Regan K, Moosavinasab S, Payne P, Lin S. Drug Repurposing Hypothesis Generation Using the "RE:fine Drugs" System. J Vis Exp 2016. [PMID: 28060329 PMCID: PMC5226396 DOI: 10.3791/54948] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The promise of drug repurposing is that existing drugs may be used for new disease indications in order to curb the high costs and time for approval. The goal of computational methods for drug repurposing is to enable solutions for safer, cheaper and faster drug discovery. Towards this end, we developed a novel method that integrates genetic and clinical phenotype data from large-scale GWAS and PheWAS studies with detailed drug information on the concept of transitive Drug-Gene-Disease triads. We created "RE:fine Drugs," a freely available, interactive dashboard that automates gene, disease and drug-based searches to identify drug repurposing candidates. This web-based tool supports a user-friendly interface that includes an array of advanced search and export options. Results can be prioritized in a variety of ways, including but not limited to, biomedical literature support, strength and statistical significance of GWAS and/or PheWAS associations, disease indications and molecular drug targets. Here we provide a protocol that illustrates the functionalities available in the "RE:fine Drugs" system and explores the different advanced options through a case study.
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Affiliation(s)
- Kelly Regan
- Department of Biomedical Informatics, The Ohio State University;
| | - Soheil Moosavinasab
- Research Information Solutions and Innovation, The Research Institute at Nationwide Children's Hospital
| | - Philip Payne
- Department of Biomedical Informatics, The Ohio State University
| | - Simon Lin
- Research Information Solutions and Innovation, The Research Institute at Nationwide Children's Hospital
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24
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Paik H, Chen B, Sirota M, Hadley D, Butte AJ. Integrating Clinical Phenotype and Gene Expression Data to Prioritize Novel Drug Uses. CPT-PHARMACOMETRICS & SYSTEMS PHARMACOLOGY 2016; 5:599-607. [PMID: 27860440 PMCID: PMC5192994 DOI: 10.1002/psp4.12108] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 08/05/2016] [Indexed: 12/22/2022]
Abstract
Drug repositioning has been based largely on genomic signatures of drugs and diseases. One challenge in these efforts lies in connecting the molecular signatures of drugs into clinical responses, including therapeutic and side effects, to the repurpose of drugs. We addressed this challenge by evaluating drug‐drug relationships using a phenotypic and molecular‐based approach that integrates therapeutic indications, side effects, and gene expression profiles induced by each drug. Using cosine similarity, relationships between 445 drugs were evaluated based on high‐dimensional spaces consisting of phenotypic terms of drugs and genomic signatures, respectively. One hundred fifty‐one of 445 drugs comprising 450 drug pairs displayed significant similarities in both phenotypic and genomic signatures (P value < 0.05). We also found that similar gene expressions of drugs do indeed yield similar clinical phenotypes. We generated similarity matrixes of drugs using the expression profiles they induce in a cell line and phenotypic effects.
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Affiliation(s)
- H Paik
- Institute for Computational Health Sciences, School of Medicine, University of California San Francisco, San Francisco, California, USA.,Department of Pediatrics, School of Medicine, University of California - San Francisco, San Francisco, California, USA
| | - B Chen
- Institute for Computational Health Sciences, School of Medicine, University of California San Francisco, San Francisco, California, USA.,Department of Pediatrics, School of Medicine, University of California - San Francisco, San Francisco, California, USA
| | - M Sirota
- Institute for Computational Health Sciences, School of Medicine, University of California San Francisco, San Francisco, California, USA.,Department of Pediatrics, School of Medicine, University of California - San Francisco, San Francisco, California, USA
| | - D Hadley
- Institute for Computational Health Sciences, School of Medicine, University of California San Francisco, San Francisco, California, USA.,Department of Pediatrics, School of Medicine, University of California - San Francisco, San Francisco, California, USA
| | - A J Butte
- Institute for Computational Health Sciences, School of Medicine, University of California San Francisco, San Francisco, California, USA.,Department of Pediatrics, School of Medicine, University of California - San Francisco, San Francisco, California, USA
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25
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Waldman SA, Terzic A. Big Data Transforms Discovery-Utilization Therapeutics Continuum. Clin Pharmacol Ther 2016; 99:250-4. [PMID: 26888297 DOI: 10.1002/cpt.322] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 12/11/2015] [Indexed: 11/09/2022]
Abstract
Enabling omic technologies adopt a holistic view to produce unprecedented insights into the molecular underpinnings of health and disease, in part, by generating massive high-dimensional biological data. Leveraging these systems-level insights as an engine driving the healthcare evolution is maximized through integration with medical, demographic, and environmental datasets from individuals to populations. Big data analytics has accordingly emerged to add value to the technical aspects of storage, transfer, and analysis required for merging vast arrays of omic-, clinical-, and eco-datasets. In turn, this new field at the interface of biology, medicine, and information science is systematically transforming modern therapeutics across discovery, development, regulation, and utilization.
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Affiliation(s)
- S A Waldman
- Department of Pharmacology and Experimental Therapeutics, Division of Clinical Pharmacology, Department of Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - A Terzic
- Mayo Clinic Center for Regenerative Medicine, Divisions of Cardiovascular Diseases and Clinical Pharmacology, Departments of Medicine, Molecular Pharmacology and Experimental Therapeutics and Medical Genetics, Mayo Clinic, Rochester, Minnesota, USA
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26
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Cichonska A, Rousu J, Aittokallio T. Identification of drug candidates and repurposing opportunities through compound-target interaction networks. Expert Opin Drug Discov 2015; 10:1333-45. [PMID: 26429153 DOI: 10.1517/17460441.2015.1096926] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
INTRODUCTION System-wide identification of both on- and off-targets of chemical probes provides improved understanding of their therapeutic potential and possible adverse effects, thereby accelerating and de-risking drug discovery process. Given the high costs of experimental profiling of the complete target space of drug-like compounds, computational models offer systematic means for guiding these mapping efforts. These models suggest the most potent interactions for further experimental or pre-clinical evaluation both in cell line models and in patient-derived material. AREAS COVERED The authors focus here on network-based machine learning models and their use in the prediction of novel compound-target interactions both in target-based and phenotype-based drug discovery applications. While currently being used mainly in complementing the experimentally mapped compound-target networks for drug repurposing applications, such as extending the target space of already approved drugs, these network pharmacology approaches may also suggest completely unexpected and novel investigational probes for drug development. EXPERT OPINION Although the studies reviewed here have already demonstrated that network-centric modeling approaches have the potential to identify candidate compounds and selective targets in disease networks, many challenges still remain. In particular, these challenges include how to incorporate the cellular context and genetic background into the disease networks to enable more stratified and selective target predictions, as well as how to make the prediction models more realistic for the practical drug discovery and therapeutic applications.
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Affiliation(s)
- Anna Cichonska
- a 1 University of Helsinki, Institute for Molecular Medicine Finland FIMM , Helsinki, Finland.,b 2 Aalto University, Helsinki Institute for Information Technology HIIT, Department of Computer Science , Espoo, Finland
| | - Juho Rousu
- c 3 Aalto University, Helsinki Institute for Information Technology HIIT, Department of Computer Science , Espoo, Finland
| | - Tero Aittokallio
- d 4 University of Helsinki, Institute for Molecular Medicine Finland FIMM , Helsinki, Finland +358 5 03 18 24 26 ; .,e 5 University of Turku, Department of Mathematics and Statistics , Turku, Finland
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Chen XW, Duan W, Zhou SF. Repurposing paclitaxel for the treatment of fibrosis: indication discovery for existing drugs. DRUG DESIGN DEVELOPMENT AND THERAPY 2015; 9:4869-71. [PMID: 26379422 PMCID: PMC4567211 DOI: 10.2147/dddt.s87771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Xiao-Wu Chen
- Department of General Surgery, The First People's Hospital of Shunde, Southern Medical University, Shunde, Foshan, Guangdong, People's Republic of China
| | - Wei Duan
- School of Medicine, Deakin University, Waurn Ponds, Victoria, Australia
| | - Shu-Feng Zhou
- Department of Pharmaceutical Science, College of Pharmacy, University of South Florida, Tampa, FL, USA
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